tbuckley/cabot-search huggingface dataset:
Abstract 2228: Genome-wide mapping of SMYD3 in HPV-negative head and neck squamous cell carcinoma
Authors: Abbas Saeed, Samantha Sevilla, Vassiliki Saloura
Journal: Cancer Research (2023)

Abstract HPV-negative head and neck squamous cell carcinoma (HNSCC) carries a particularly poor prognosis and novel therapeutic targets are thus urgently needed. We recently found that SET and MYND domain-containing 3 (SMYD3), a protein methyltransferase which has been reported to regulate global levels of trimethylated H3K4 (H3K4me3), an activating mark, and H4K20 (H4K20me3), a repressive mark, is overexpressed in HPV-negative HNSCC. Furthermore, we found that SMYD3 depletion impaired the colony formation capacity, cell cycling and the proliferation of HPV-negative HNSCC cell lines. Additionally, SMYD3 KO cell lines demonstrated decreased migratory potential. Accordingly, NSG xenograft mouse models of SMYD3 KO cell lines exhibited significantly decreased tumor growth compared to a parental HPV-negative HNSCC cell line. Based on the above preliminary results, this study aims to elucidate the specific mechanism(s) through which SMYD3 regulates the proliferative and migratory capacity of HPV-negative HNSCC cells. Nuclear/cytoplasmic fractionation of a panel of HPV-negative HNSCC cell lines showed that SMYD3 is expressed both in the nuclear as well as the cytoplasmic compartments. siRNA-mediated knockdown of SMYD3 for 6 days induced A 40% decrease in global H3K4me3 and more than 80% decrease in global H4K20me3 levels. Genome-wide mapping of SMYD3, H3K4me3 and H4K20me3 was pursued using CUT&amp;RUN assays in parental and SMYD3 KO cell lines. The GoPeaks software was utilized to call significant peaks affected by 30% (p.adj&amp;lt;0.05). 515 genes were annotated to H3K4me3 peaks and were found to have significantly decreased H3K4me3 peaks with concordant mRNA downregulation by more than 30%. 185 genes were annotated to H4K20me3 peaks and were found to have significantly decreased H4K20me3 peaks with concordant mRNA upregulation by more than 30%. Amongst these genes, cell cycle regulators and EMT genes were identified. SMYD3 peaks were called successfully and analysis of its genome-wide mapping is ongoing, with particular focus on cell cycle and EMT genes. To assess whether SMYD3 regulates the global H3K4me3 and H4K20me3, mass spectrometry analysis in SMYD3 KO cells has been conducted and analysis is ongoing. Validation of candidate genes directly regulated by SMYD3, H3K4me3 and H4K20me3 is planned by qPCR and Western blotting. This study is the first to report genome-wide mapping results of human SMYD3, and provides mechanistic insights into the oncogenic function of SMYD3 in HPV-negative HNSCC. Citation Format: Abbas Saeed, Samantha Sevilla, Vassiliki Saloura. Genome-wide mapping of SMYD3 in HPV-negative head and neck squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2228.
Abstract 6652: Overcoming immune resistance in DNA mismatch repair deficient tumors
Authors: Guillaume Mestrallet
Journal: Cancer Research (2023)

Abstract Patients with Lynch Syndrome, an inherited mismatch repair deficiency, have an increased risk for developing microsatellite unstable (MSI-H) cancers. Our team recently identified shared immunogenic frameshift peptides in patient tumors that can be targets of T cell surveillance and preventative MSI-H cancer vaccines. We hypothesize that in Lynch Syndrome some premalignant lesions are capable of evading immune surveillance from cytotoxic T lymphocytes due to immune checkpoint expression and immunosuppression from tumor, myeloid and stromal cell populations. Immune checkpoint blockade (ICB) showed promising results in the treatment of MSI-H tumors and are being evaluated in the adjuvant setting of patients with Lynch syndrome post surgical resection. However, a significant percentage of advanced MSI-H tumors resist ICB suggesting evolving mechanisms of immune resistance. We will use a MSI-H in vivo mouse model and additionally develop 3D spheroids cocultured with immune cells to characterize the underlying immune resistance mechanisms. The MSI-H mouse model will first be applied to identify shared frameshifts in MSI-H tumors by WES to develop vaccination approaches preventing tumor growth. Then, we will quantify MSI-H tumor growth and immune infiltration in the MSI-H mouse model, with or without ICB. We will analyze the presence of immunosuppressive pathways and myeloid subsets in high growth resisting tumors by immunohistochemistry, scRNAseq, spatial transcriptomics and flow cytometry. In addition, we will perform short-term in vitro spheroid-splenic cell co-cultures to better characterize the early immune resistance mechanisms. We will also perform these spheroid-immune cell co-cultures using the immune cells taken from mice after vaccination or ICB to identify the early myeloid immune resistance mechanisms. Overall, the identification of shared immune frameshifts in MSI-H tumors will allow developing peptide vaccination approaches to prevent tumor growth. Further, the identification of myeloid resistance pathways will guide therapeutic strategies against tumor resisting to ICB and/or vaccination. Citation Format: Guillaume Mestrallet. Overcoming immune resistance in DNA mismatch repair deficient tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6652.
Abstract 5646: Spatial transcriptomic profiling of the human and mouse retina prepared with CryoJane Tape Transfer System using GeoMx and CosMx spatial analysis
Authors: Charles Glaser, Su Ma, Wei Yang, Yan Liang, Joeseph Beechem, Vera L. Bonilha, Sujata Rao, William Horrigan, Bela Anand-Apte
Journal: Cancer Research (2023)

Abstract The goal of this study is to identify key transcriptomic markers within layers of the retina by individually profiling layers using cellular and subcellular spatial transcriptomics, additionally, comparing the results between each level. Both human and mouse retina samples, prepared fresh frozen and fixed frozen, are analyzed using the GeoMx® Digital Spatial Profiler (DSP) and CosMx® Spatial Molecular Imager (SMI) using the whole mouse transcriptome atlas and 1000-plex mouse neuro panel, respectively. Samples are fixed using Cryo-Jane Taper Transfer system. Samples are mounted on to adhesive coated slides as well as adhesive tape to mount samples to glass slides. This method is used to secure fragile frozen tissue, such as the retina. Human and mouse samples were stained using immunofluorescent microscopy targeting neurofilament H (NF-H), glial fibrillary acidic protein (GFAP) and NeuN on DSP and 18s rRNA, amyloid-beta and GFAP on SMI. Staining allows for identification of structural layers in the retina. Simultaneously, regions of interest (ROI) for spatial profiling are selected based on immunofluorescent stains. On DSP, each sample had 3x ROIs in the photoreceptor layer, inner nuclear layer and ganglion cell layer, then, oligonucleotides were collected and sequenced. Finally, raw counts were Q3 normalized for analysis. For SMI data analysis, 6 field of views (FOVs) were put on each section to cover most regions with multiple layers. ~8000 genes were detected on human retina samples using DSP. Around 500 unique genes were detected between the photoreceptor and inner nuclear layer using DSP. Preliminary SMI results show we were able to identify cell types (amacrine, horizontal cell, biopolar cell, ganglion cell, etc) and cell specific markers for outer nuclear layer, inner nuclear layer and ganglion cell layer. Data between DSP and SMI showed high concordance with one another, identifying many genes in each layer. Citation Format: Charles Glaser, Su Ma, Wei Yang, Yan Liang, Joeseph Beechem, Vera L. Bonilha, Sujata Rao, William Horrigan, Bela Anand-Apte. Spatial transcriptomic profiling of the human and mouse retina prepared with CryoJane Tape Transfer System using GeoMx and CosMx spatial analysis. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5646.
Abstract 2607: Homogenous TP53mut-associated tumor biology across mutation and cancer types revealed by comprehensive mRNA expression analysis
Authors: Jan Budczies, Eva Romanovsky, Klaus Kluck, Iordanis Ourailidis, Michael Menzel, Susanne Beck, Markus Ball, Daniel Kazdal, Petros Christopoulos, Peter Schirmacher, Thorsten Stiewe, Albrecht Stenzinger
Journal: Cancer Research (2023)

Abstract TP53 mutations are the most common single gene alteration in human cancer with diagnostic and prognostic implications in some cancer types. While no TP53-targeting therapeutics have been approved in the USA or Europe yet, drugs tailored to specific TP53 mutations, restoring the functionality of mutated TP53 (TP53mut), and protecting TP53 from negative regulation are being explored in preclinical studies and clinical trials. We performed a comprehensive mRNA expression analysis in 24 cancer types of the TCGA to extract (i) a consensus expression signature shared across TP53 mutation types and cancer types, (ii) differential gene expression patterns between different TP53 mutation types such as LOF, GOF, as well as dominant-negative mutations, and (iii) cancer types specific gene expression patterns. Mutational hotspots showed a similar pattern across cancer types, but at the same time prevalence was significantly different between cancer types for about half of the most prevalent hotspots. Both can be explained in part by the mutational processes operational for example the clock-like process behind SBS1 that is operational across cancer types and aflatoxin exposure assocated with SBS24 that ist operational in liver hepatocellular carcinoma. Virtually no genes were differential between tumors harboring different types of TP53 mutations in none of the cancer types, while hundreds of genes were over- and underexpressed in TP53mut compared to TP53wt tumors. A consensus gene list of 178 common over- and 32 common underexpressed genes was shared between at least two-thirds of the 24 cancer types. Analysis of the immune tumor microenvironment revealed exclusively decreased immune cell populations in the TP53mut tumors in six, a mixed pattern in four, exclusively increased immune cell populations in two, and no significant alterations in 20 cancer subtypes. The analysis of a large cohort of human tumors complements results from experimental studies and support the development of novel strategies for therapeutic targeting of TP53mut. Citation Format: Jan Budczies, Eva Romanovsky, Klaus Kluck, Iordanis Ourailidis, Michael Menzel, Susanne Beck, Markus Ball, Daniel Kazdal, Petros Christopoulos, Peter Schirmacher, Thorsten Stiewe, Albrecht Stenzinger. Homogenous TP53mut-associated tumor biology across mutation and cancer types revealed by comprehensive mRNA expression analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2607.
Abstract 4640: CAF contributes to cancer progression through its immunomodulatory role within the tumor microenvironment
Authors: Muriel Antonieta Núñez, Oreste Corrales, Victoria Velasquez, Daniel Ernst, Montecinos Viviana, Francisco Nualart, María Isabel Yuseff, Javier Cerda-Infante
Journal: Cancer Research (2023)

Abstract Introduction: Cancer progression and metastatic spread is modulated by the tumor microenvironment. Cancer-associated fibroblasts (CAF) are the most abundant cell type within the tumor microenvironment. Little is known about the specific mechanisms by which CAF would exert its cancer progression, through the high secretory capacity of soluble pro-tumorigenic molecules and remodeling of the extracellular matrix. Recent studies in our laboratory have shown for the first time that CAF derived from patients without metastasis express a different genetic profile than those with metastases (mCAF). This study seeks to evaluate the contribution of mCAF to tumor progression through its immunomodulatory role. Methodology: mCAFs were obtained from patients with metastatic disease and BAF from benign patients. The fibroblasts were functionally characterized by the generation of fibroblast-derived matrices (FDM) and secretory profiles by cytokine array. CD8 T lymphocytes were obtained from healthy patients and treated with fibroblast-secretome. Markers were studied by flow cytometry: activation (CD25 and CD69) and repression (LAG3 and PD1). The migration of CD8 T lymphocytes was studied by transwell and agarose drop migration assay. Results and conclusion: FDM of mCAF are different in their composition and organization. Furthermore, the secretome of each type of fibroblast presents a differential effect on the activation of CD8 T cells according to the markers highlighted. Regarding migration, it has been observed that the mCAF-secretome can attract lymphocytes. However, it would lead them to apoptosis. Our results suggest that mCAF, within the tumor microenvironment, has an immunomodulatory role on CD8 T lymphocytes. Acknowledgment: Beca Doctorado Nacional ANID 21181427 Citation Format: Muriel Antonieta Núñez, Oreste Corrales, Victoria Velasquez, Daniel Ernst, Montecinos Viviana, Francisco Nualart, María Isabel Yuseff, Javier Cerda-Infante. CAF contributes to cancer progression through its immunomodulatory role within the tumor microenvironment. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4640.
Abstract 2586: Oncogenic<i>PIK3CA</i> promotes hematopoietic reprogramming and cell transdifferentiation developing hematopoietic malignancy
Authors: Emma Kozurek, Erin B. Dickerson, Jong Hyuk Kim
Journal: Cancer Research (2023)

Abstract PIK3CA mutation is one of the most common, recurrent genetic abbrations identified across multiple types of cancers. Such mutations sustain activation of PI3K/AKT/mTOR pathway, being considered reliable therapeutic targets; yet, the functional consequences still remain unclear. Angiosarcomas are a heterogenous group of soft-tissue sarcomas that form malignant endothelium with disorganized, irregular blood-filled vascular spaces, and a subset of the vascular tumors harbor PIK3CA mutations. In this study, we found that one of 11 canine angiosarcoma cells gave rise to vascular tumors in 3 of 3 mice in a series of xenograft experiments using a total of 86 immunodeficient BNX mice. Intriguingly, we also observed that xenografts developed lymphoproliferative tumors indicating a mouse B-cell origin in 3 of 4 mice from one case of canine patient-derived tumor xenografts: four tumor cases surgically implanted in a total of 16 BNX mice. Additionally, canine angiosarcoma cells induced splenomegaly with expansion of Ter-119+ erythroid progenitors in NSG mice. Canine angiosarcoma cells (two cell lines; DHSA-1426 and EFB) were capable of hematopoietic expansion and cell lineage differentiaton in vitro. Since PIK3CA mutations appear to promote cellular stemness and impairment of cell lineage differentiation, we determined if the mutations play a role in hematopoietic regulations of angiosarcoma cells. DHSA-1426 angiosarcoma cells were used to induce PIK3CA H1047R mutations using CRISPR/Cas9. We found that PIK3CA mutant angiosarcoma cells dysregulated AKT, ERK, and mTOR pathway with enrichement of inflammatory cytokines such as IL-6, IL-8, and MCP-1. Single cell RNA-seq data showed that PIK3CA mutant angiosarcoma cells established distinct single cell clusters representing immune reactions, cellular stemness, and lineage differentiation. Furthermore, PIK3CA mutant angiosarcoma cells developed malignant hematopoietic tumor in one of five BNX mice, while no evidence of hematopoietic tumor formation was found in mice transplanted with non-mutant cells. Altogether, our data suggest that angiosarcoma cells have the capacity to promote hematopoietic imbalance impacting on cellular ontogeny and lineage differentiation, potentially mediated by oncogenic PIK3CA. Our ongoing work is determining the mechanism of the cell fate decisions using bi-potential hematoendothelial progenitors derived from induced pluripotent stem cells harboring oncogenic PIK3CA. Citation Format: Emma Kozurek, Erin B. Dickerson, Jong Hyuk Kim. OncogenicPIK3CA promotes hematopoietic reprogramming and cell transdifferentiation developing hematopoietic malignancy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2586.
Abstract 1742: Cediranib reverses taxane resistance in CLIP-170S expressing gastric cancer
Authors: William G. Stone, Urko del Castillo, Prashant V. Thakkar, Manish A. Shah, Paraskevi Giannakakou
Journal: Cancer Research (2023)

Abstract Taxane-based chemotherapy is a first-line treatment for patients with Gastric Cancer (GC), however, many will not respond due to mechanisms of resistance. Recently, we reported the discovery of a novel truncated variant of the microtubule plus-end binding protein CLIP-170, hereafter CLIP-170S, whose expression is enriched in taxane-resistant cell lines and in 65% of patients with GC, non-responsive to Cabazitaxel monotherapy. CLIP-170S knockdown reversed taxane resistance and its ectopic expression led to resistance, suggesting causation. Computational analysis of RNA-seq data in conjunction with the connectivity map from taxane-sensitive and -resistant GC cell lines, predicted imatinib as the top candidate drug to overcome drug resistance. Imatinib treatment completely reversed taxane resistance, experimentally confirming the prediction, and did so unexpectedly by selective depletion of CLIP-170S. Other RTK inhibitors, such as Sunitinib, Ponatinib, Axitinib, and Cediranib also depleted CLIP-170S, suggesting a class effect, however, the mechanism is unknown. To investigate the mechanism of RTKi induced depletion of CLIP-170S, we sought to investigate the involvement of proteasomal and lysosomal cellular compartments. Preliminary results indicated that treatment of CLIP-170S expressing cells with Imatinib or Cediranib led to an increase in lysosome size, suggesting increased lysosomal activity. In parallel, we are testing in-vivo the synergistic activity of the RTKi, Cediranib, in combination with docetaxel in GC tumors expressing CLIP-170S. Together, these results will allow us to implement a novel clinical trial for patients with GC by using Cediranib as a treatment to increase taxane efficacy through CLIP-170S depletion. Citation Format: William G. Stone, Urko del Castillo, Prashant V. Thakkar, Manish A. Shah, Paraskevi Giannakakou. Cediranib reverses taxane resistance in CLIP-170S expressing gastric cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1742.
Abstract 26: BaF3 RAS cell panel, a powerful cell model for Ras inhibitor discovery and development
Authors: PENG YAO, Yu Wang, Chang Liu, Na Wang, Wei Meng, Jinying Ning, Feng Hao
Journal: Cancer Research (2023)

Abstract RAS, abbreviated from Rat sarcoma virus, is composed of three small GTPase proteins, HRAS, KRAR and NRAS. Over-activation of these genes due to different mutation were found in up to 20% of all human cancers and about 90% in pancreatic cancer. The identification of RAS mutation, especially KRAS-G12S or G12D mutation, as cancer diver genes has recently led to rapid development of anti-tumor therapeutics agents such as sotorasib (AMG 510), adagrasib (MRTX-849) and MRTX1133, but there are still no good drugs for the cancer patients with other RAS mutations. Ba/F3 line is a popular cell model for studying both kinases and their inhibitors, because some kinases can render the growth of Ba/F3 cells to be depended on the over-activation of the kinases instead of exogenous IL-3 supplement, while their inhibitors can antagonize these effects. Our group has generated a Ba/F3 RAS cell panel with 29 KRAS, 11 HRAS and 20 NRAS different single or double mutants for RAS inhibitor screening and development, all of these lines were well validated with PCR sequencing, Western Blot and KRAS G12C and G12D inhibitors. In addition to use the cell lines for in vitro assays, the transformed Ba/F3 lines can grow well in immune-deficient mice as in vivo models. Our data indicate that the cell line panel of Ba/F3 is a powerful system for new RAS inhibitor discovery and development. Citation Format: PENG YAO, Yu Wang, Chang Liu, Na Wang, Wei Meng, Jinying Ning, Feng Hao. BaF3 RAS cell panel, a powerful cell model for Ras inhibitor discovery and development [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 26.